Kocarek - Pharmacogenetics Flashcards
Pharmacogenetics/Pharmacogenomics definition:
study of genetically controlled variations in drug response, and includes both genetic polymorphisms and rare genetic defects that alter an individual’s drug response
Genetic Polymorphisms
a Mendelian or monogenic trait that exists in the population in at least two phenotypes, neither of which is rare (>1-2%)
What is used to treat acute lymphoblastic leukemia and what gene variation prevents metabolism and can be fatal?
6-mercaptopurine (6-MP) is used to treat childhood ALL.
1 in 300 children has a variant gene for thiopurine methyltransferase that prevents 6-MP metabolism; drug accumulates in those children and can be fatal
What is clopidogrel and what does it require for conversion to its active form?
clopidogrel (plavix) is an anti-platelet drug that is used in addition to aspirin to prevent CV events in high risk pts.
Requires metabolism by CYP2C19 for conversion to active form
Without CYP2C19, clopidogrel builds up, therefore you need to know if the pt is a CYP2C19 poor metabolizer
What is the cause of isoniazid-induced neuropathy in some individuals?
NAT2 deficiency
What causes prolonged apnea after succinylcholine?
pseudocholinesterase deficiency
What breaks down debrisoquine (anti-hypertensive used in 1975 by Dr. Robert Smith)? What is the product?
Debrisoquine is converted to 4-hydroxydebrisoquine (inactive metabolite) by CYP2D6
Ultrarapid metabolizer for debrisoquine
multiple copies of CYP2D6
How can one estimate the fraction of phenotypic variability that is attributable to genetic factors?
Twin studies - monozygotic vs. dizygotic
Multigenerational kindred studies - interfamily vs. intrafamily variability
Additive (Codominant) Traits
Most common pattern
No domination of one allele over the other
Gene dosage effect
o AA= 2 good alleles, 100% function
o Aa= 1 good allele and 1 mutant allele, 50% function
o Aa= 2 mutant alleles, little/no function
Ex: CYP2C19 poor metabolizer
Autosomal Recessive
Normal allele dominates over mutant allele
o AA= 100% function
o Aa= 100% function
o aa= little/no function
Ex: CYP2D6 poor metabolizer
Autosomal Dominant
Only those with both good alleles have normal activity
o AA=100% function
o Aa and aa= little/ no function
What is the recommended starting dose for warfarin determined by?
CYP2C9 - metabolizes and inactivates warfarin
VKORC1 - pharmacological target of warfarin
Major types of polymorphism (3)
Single nucleotide polymorphisms (SNPs)
Insertions/deletions (Indels)
Copy number variations (CNV)
Single nucleotide polymorphisms (SNPs)
One every few hundred
About 10 million SNPs
Copy number variations (CNV)
~10% of the genome
Segment of DNA in which a variable number of that segment has been found in one or more populations
Duplications, deletions, inversions
CYP2D6 duplications associated with ultrarapid metabolizer phenotype
cSNPs
Types:
SNPs in coding region
Non-synonymous (missense) - aa change
Synonymous (sense) - no aa change
Nonsense - stop codon
Polymorphisms in non-coding regions (4)
5’ and 3’ untranslated regions of mRNA
Promoter and enhancer regions of genes
Introns
Intergenic regions
Polymorphisms in 5’ and 3’ untranslated regions of mRNA
may alter cis-elements that determine mRNA translatability or stability
Polymorphisms in Promoter and enhancer regions of genes
may alter cis-elements that regulate gene transcription
Polymorphisms in introns
When near exon-intron boundaries, may affect transcript splicing - would often introduce a frame shift and a premature stop codon
Polymorphisms in intergenic regions
may affect DNA tertiary structure, interaction with chromatin and topoisomerases, or DNA replication
Where are most of the SNPs?
most of the SNPs are within introns or intergenic regions.
What does CYP3A5*3 indicate?
The CYP3A5*3 allele contains a SNP in intron 3 that creates an alternative splice site, which results in introduction of an early stop codon and production of an inactive protein.
Haplotype
Haplotype - a set of SNPs on a single chromosome that is statistically associated
The particular combination of all variants that occurs together for a gene
(wiki) A combination of alleles (DNA sequences) at adjacent locations (loci) on a chromosome that are inherited together.
A gene is likely to have more than one SNP – the haplotype is the particular combination of all SNPs
ABCB1 gene has SNPs at base pair 3421 (T or A) and 3435 (C or T), what are the possible haplotypes?
The possible haplotypes would be: • T3421C3435 • T3421T3435 • A3421C3435 • A3421T3435
Linkage definition:
2 types:
Definition: The extent to which the genotypes at two genetic loci are independent of one another.
Linkage equilibrium – the genotype present at one locus is independent of the genotype at a second locus
Linkage disequilibrium – the genotypes at the two loci are not independent of one another
Note:In complete linkage disequilibrium, genotypes at two loci always occur together
Penetrance
Penetrance: proportion of individuals carrying a variant allele that express an associated phenotype
Clinical relevance of a polymorphism is determined by (4):
Frequency and penetrance of a variant allele
Narrowness of therapeutic index or sharpness of dose-response curve
Limited availability of alternative clearance pathways
Absence of alternative drugs
What type of varient has the highest predicted risk to the phenotype?
Nonsense
What types of genes are involved in pharmacogenetic traits?
Genes that encode determinants of a drug’s pharmacokinetics
o e.g., Drug-metabolizing enzymes, transporters
Genes that encode drug receptors and targets
o Variants with profound functional consequences may cause disease
phenotypes that cause negative selective pressure
o However, variants that cause more subtle changes can be maintained in a
population without causing disease but may cause variation in drug
response
Genes that are involved in the disease being treated but do not directly interact
with a drug (modifiers)
(determinants, receptor/target, disease but don’t interact with drug)
Why is UGT1A1 important?
What happens with a UGT1A1 defect?
What are some genetic diseases attributable to UGT1A1?
it metabolizes bilirubin
hyperbilirubinemia
Specific genetic diseases
that are attributable to UGT1A1 polymorphisms include Crigler-Najjar syndrome types I
and II and Gilbert’s syndrome.
What 2 enzymes catalyze N-acetylation?
Which one is the primary polymorphic one?
Two major enzymes catalyze N-acetylation– N-acetyltransferases 1 and 2 (NAT1 and NAT2)
NAT2 is primary one that is polymorphic
NAT1 was thought not to be polymorphic, but recent evidence suggests that it also exhibits genetic polymorphisms
N-acetyltransferases 2 (NAT 2) catalyzes: (3 examples)
NAT2 catalyzes the N-acetylation of a large number of drugs and environmental chemicals: e.g., procainamide, caffeine, 4-aminobiphenyl (human bladder carcinogen)
• NAT2 shows considerable ethnic variation: Slow acetylators account for 90% in other groups
Acetylation polymorphism: slow acetylators
Slow acetylation is associated with several clinically important consequences (3):
isoniazid tx:
sulfa drug tx:
arylamin carcinaogens:
Slow acetylators more prone to polyneuropathy during isoniazid treatment
Slow acetylators more likely to develop hemolytic anemia during treatment with sulfa drugs
Incidence of bladder cancer greater in slow acetylators exposed to arylamine carcinogens
What is a consequence of fast acetylators?
“Fast” acetylators require larger doses to achieve a given desired effect
Human acetylation polymorphism controlled by 4 major alleles at a single autosomal gene locus on:
Slow vs. Fast acetylation:
Dominance:
Human acetylation polymorphism controlled by 4 major alleles at a single autosomal gene locus on chromosome 8
o 3 alleles encode for slow activity; 1 allele encodes for fast activity
o Fast activity is dominant – an individual must have 2 slow alleles to be a slow acetylator
How many ADH enzymes in humans? Classes? Which class is the major ethanol-metabolizing enzyme?
Humans have 7 ADH enzymes grouped into 5 classes (I-V)
o Class I enzymes are major ethanol-metabolizing enzymes
Nomenclature:
ADH1 =
ADH2 =
ADH3 =
Nomenclature:
ADH1 = ADH1A, encodes α polypeptide
ADH2 = ADH1B, encodes β polypeptide
ADH3 = ADH1C, encodes γ polypeptide
Comparison of ADHs in Caucasians, East Asians, and individuals of African descent
Majority of Caucasians (about 95%) have ADH21 allele; about 50% ADH31 and ADH3*2
Majority of Japanese, Chinese, and Koreans have ADH2*2 allele
ADH23 observed in ~15% of individuals of African descent; rest have ADH21;
ADH3*1 in ~95%
Comparison between ADH22 and ADH21.
What other polymorphism may occur with ADH2*2?
Individuals with the ADH22 genotype metabolize ethanol more rapidly than do those with the ADH21. Faster ethanol metabolism results in
increased production of acetaldehyde, which is the toxic metabolite that causes alcohol induced
flushing.
Some individuals also have a polymorphism in the aldehyde dehydrogenase enzyme (ALDH2*2) that decreases its ability to convert the acetaldehyde into acetic acid. Since these individuals both produce more acetaldehyde and are less able to detoxify it, they are particularly prone to flushing.
ADH Genotype/Isoenzyme
ADH21 - beta1beta2
ADH22 - beta2beta2
ADH2*3 - beta3beta3
EtOH to Acetyl-CoA formula
EtOH –ADH–> Acetaldehyde (Toxic) –ALDH–>Acetic acid —-> Acetyl-CoA
What ADH genotype has the highest/lowest Vmax?
Highest = 400 min-1: ADH2*2 Lowest = 9 min-1: ADH2*1
